Mich Ard wrote:
> I'm currently making a phylogenetic tree
> based on the protein sequences, using the
> programs of clustalW and phylip, and found
> the output is "unstable", it's always changing
> depending on the inputing order of these
> sequences;
- Mich,
you should be aware that the apparent instability may in fact merely be
different graphical representations of the exact same tree. Remember that even
if you rotate a branch then it's
still the same tree topology.
I just experimented with using the differently ordered versions of one distance
matrix as input to neighbor (of the phylip package). This results in trees that
are topologically identical, but that are rendered differently by drawtree (also
phylip package). This is mainly due to a different orientation of the entire
tree, and also due to some branches being rotated.
The bottom line: identical trees may look different depending on how you draw
them.
Hope this helps,
- Anders
--
Anders Gorm Pedersen, Ph.D. (gorm at cbs.dtu.dk)
Technical University of Denmark
